Contacts of the helix formed by residues 264 - 278 (chain A) in PDB entry 3KSA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A MET 3.9 4.5 + - - -
109A ASP 3.6 2.1 + - - -
110A GLY* 3.5 29.3 - - - -
262A GLU 4.3 0.2 + - - -
263A ILE* 1.3 79.1 - - + +
265A LYS* 1.3 66.6 + - - +
266A ALA* 2.8 12.1 + - - +
267A ASN* 2.9 40.8 + - + +
268A LEU* 2.9 20.8 + - - +
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A MET* 3.4 27.8 + - + +
109A ASP* 3.3 18.8 - - - +
259A ILE* 3.9 18.9 - - + +
263A ILE 3.5 6.7 + - - -
264A ASN* 1.3 68.9 - - - +
266A ALA* 1.3 61.7 + - - +
268A LEU* 3.4 6.5 + - - +
269A VAL* 3.0 23.8 + - + +
289A ASP* 2.9 30.7 - - - +
291A SER* 3.4 27.8 - - - -
296A LEU* 3.9 24.7 - - + -
298A ILE* 4.5 13.7 - - + -
447D ARG* 5.1 0.7 - - - +
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 3.1 42.3 - - + +
264A ASN* 2.8 9.3 + - - +
265A LYS* 1.3 78.3 - - - +
267A ASN* 1.3 70.0 + - - +
269A VAL* 3.1 14.6 + - - +
270A LYS* 3.2 10.7 + - - +
289A ASP* 5.9 0.7 - - - -
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Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ASN* 2.9 34.0 + - + +
266A ALA* 1.3 74.9 - - - +
268A LEU* 1.3 66.8 + - - +
270A LYS* 3.0 9.8 + - + +
271A LYS* 2.8 30.2 + - + +
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ILE* 4.6 6.7 - - + -
263A ILE* 4.5 16.9 - - + +
264A ASN 2.9 16.9 + - - +
265A LYS* 3.4 9.4 - - - +
267A ASN* 1.3 76.8 - - - +
269A VAL* 1.3 62.4 + - - +
271A LYS* 3.5 6.0 + - + +
272A ILE* 3.2 30.1 + - + +
298A ILE* 4.0 24.0 - - + -
319A THR* 4.3 8.3 - - - +
320A ASP* 3.8 42.0 - - + +
321A LEU* 3.8 27.1 - - + +
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LYS* 3.0 15.1 + - + +
266A ALA* 3.1 10.3 + - - +
268A LEU* 1.3 75.2 - - + +
270A LYS* 1.3 69.3 + - - +
272A ILE* 3.1 8.8 + - - +
273A ASP* 3.1 21.9 + - + +
287A VAL* 5.0 10.5 - - + +
288A ARG 5.4 0.7 - - - +
289A ASP* 4.0 28.7 - - + +
298A ILE* 3.8 38.4 - - + -
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Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ALA 3.2 7.0 + - - +
267A ASN* 3.0 12.6 + - - +
269A VAL* 1.3 80.1 - - - +
271A LYS* 1.3 59.5 + - - +
273A ASP* 3.1 8.0 + - - +
274A ASP* 2.8 31.4 + - - +
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ASN* 2.8 21.4 + - + +
268A LEU* 3.7 8.3 - - + +
270A LYS* 1.3 72.2 - - - +
272A ILE* 1.3 60.9 + - - +
274A ASP* 3.5 11.0 - - + +
275A VAL* 3.4 21.8 + - - +
318A TYR* 2.8 29.5 + - - +
319A THR* 3.5 22.0 - - + +
320A ASP* 5.5 2.9 - - + +
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 4.6 4.3 - - + -
268A LEU* 3.2 23.7 + - + +
269A VAL* 3.1 10.4 + - - +
270A LYS 3.1 0.8 - - - -
271A LYS* 1.3 73.5 - - - +
273A ASP* 1.3 62.3 + - - +
275A VAL* 2.8 31.9 + - + +
276A ARG* 3.4 3.1 + - - +
287A VAL* 3.7 17.3 - - + -
298A ILE* 5.4 4.7 - - + -
300A ILE* 3.5 37.0 - - + -
315A LEU* 4.1 16.8 - - + -
319A THR* 4.4 12.3 - - + +
321A LEU* 4.0 24.9 - - + -
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Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A VAL* 3.1 9.9 + - + +
270A LYS* 3.1 10.1 + - - +
272A ILE* 1.3 78.6 - - - +
274A ASP* 1.3 65.2 + - - +
276A ARG* 3.0 43.6 + - - +
277A VAL* 3.0 25.1 + - - +
287A VAL* 3.7 30.5 + - + +
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Residues in contact with ASP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LYS 2.8 16.4 + - - +
271A LYS* 3.5 14.6 - - + +
273A ASP* 1.3 76.1 - - - +
275A VAL* 1.3 56.8 + - - +
277A VAL* 4.1 6.3 - - - +
278A ASN* 3.0 34.0 + - - +
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LYS* 3.4 13.2 + - - +
272A ILE* 2.8 15.5 + - + +
274A ASP* 1.3 79.6 - - - +
276A ARG* 1.3 66.2 + - - +
278A ASN* 4.9 0.4 - - - -
279A ASN* 3.0 15.8 + - - -
280A LYS* 3.0 20.3 + - + -
281A VAL* 4.4 17.0 + - + +
284A ILE* 4.4 12.3 - - + +
314A TYR* 3.9 26.0 - - + +
315A LEU* 4.5 13.2 - - + -
318A TYR* 5.2 2.2 - - + -
319A THR* 4.4 16.2 - - + -
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ILE* 3.4 1.7 + - + +
273A ASP* 3.0 45.9 + - - +
275A VAL* 1.3 81.2 - - - +
277A VAL* 1.3 87.6 + - - +
279A ASN* 2.6 28.2 + - - +
284A ILE* 3.5 30.1 - - + +
285A ALA 3.4 32.3 + - - +
287A VAL* 4.9 5.2 - - + +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASP* 3.0 16.5 + - - +
274A ASP* 4.1 6.7 - - - +
276A ARG* 1.3 107.0 - - - +
278A ASN* 1.3 63.2 + - + +
279A ASN* 2.9 11.3 + - - +
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Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ASP 3.0 18.8 + - - +
275A VAL* 4.1 2.7 - - - +
277A VAL* 1.3 79.1 - - + +
279A ASN* 1.3 68.7 + - - +
280A LYS* 2.9 13.0 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il